The intraseasonal variability (ISV; 20-90 days) in Makassar Strait, the primary pathway for Pacific water flow into the Indian Ocean and a waveguide for transmitting subinertial energy from the tropical Indian Ocean to Indonesian seas, is investigated, using the 2004-2006 International Nusantara Stratification and Transport (INSTANT) observations. The INSTANT current and temperature timeseries in the Labani Channel, a narrow constriction in Makassar Strait, are used to identify the ISV. Additionally, insitu current measurements along with satellite-derived wind and sea level anomaly data in the region are employed to track the transmission of ISV from their likely origin. We find that the Makassar Strait ISV can be classified as locally or remotely forced features. Local winds and shear flow instability-generated eddies within Makassar Strait control the locally forced ISV component, while the remotely forced part is linked to equatorial Indian Ocean Kelvin waves and Sulawesi Sea eddies. The oceanic response to the local wind stress varying at periods of 45-90 days, with 60-day oscillation showing the strongest coherence, is constrained to along-strait flow primarily within the upper 50 m of the water column. At depths greater than 50 m, we observe that the 20-40 day variability reflects locally generated eddy signatures, while the 60-90 day variability agrees with remotely forced Kelvin wave characteristics. Moreover the Sulawesi Sea ISV, signifying eddy signatures, and along-strait flow across the Makassar Strait pycnocline of 50-450 m display significant coherence at periods of 45-90 days. The observed 60-90 day variability at depths of 100-450 m, coinciding with weaker Makassar Strait throughflow, exhibits Kelvin wave signatures including vertical energy propagation, energy equipartition, non-dispersive relationship and semi-geostrophic balance. Current meters at 750 m and 1500 m further provide evidence that the vertical structure of the Kelvin waves resembles that of a second baroclinic mode. We propose that the intraseasonal Kelvin waves emanate from the tropical Indian Ocean as wind-forced equatorial Kelvin waves and propagate along a waveguide which extends from the southwestern coasts of the Indonesian archipelago to Makassar Strait, via Lombok Strait. From Lombok Strait to Makassar Strait, the Kelvin waves navigate along the 100-m isobath. The intraseasonal Kelvin waves induce increased vertical shear of the along-strait flow across the pycnocline, which potentially leads to instability with a vertical mixing rate of 1-5x 10^-5 m^2s. Moreover the intraseasonal Kelvin waves also force the ITF transport anomalies in Makassar Strait. The 20-40 day variability is most evident in the across-strait flow, and in the across-strait gradient of the along-strait flow as well as in the vertical displacements of isotherms observed at depths of 100-300 m. The flow fields at 20-40 days are approximated by a vortex velocity structure, and the corresponding isotherm displacements signify potential vorticity conservation. We propose that southward-advected eddies, generated in the northern Makassar Strait at latitudes of 0.5-2S due to background flow instability, likely explain the 20-40 day variability observed in the Labani Channel.